Applications of next-generation sequencing technologies in functional genomics

Morozova, Olena; Marra, Marco A.

doi:10.1016/j.ygeno.2008.07.001

Cited by 1,008 publications

(694 citation statements)

References 110 publications

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“…Nevertheless, the same technologies employed for DNA-based analyses can be used to interrogate a variety of other disease-relevant processes, including RNA expression, alterations in splicing, epigenetic regulation, and protein-nucleotide interactions (eg: transcription factor binding) 93 . These applications hold considerable future diagnostic and clinical potential and are already providing great utility for investigators applying comprehensive system-based approaches to the study of CHD 94,95 .…”

Section: Future Developmentsmentioning

confidence: 99%

Genetics and Genetic Testing in Congenital Heart Disease

Cowan

Ware

2015

Clinics in Perinatology

118

122

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Section: Future Developmentsmentioning

confidence: 99%

Genetics and Genetic Testing in Congenital Heart Disease

Cowan

Ware

2015

Clinics in Perinatology

118

122

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“…7 These important characteristics permit the ultra-deep sequencing technologies to be widely used in the field of biology and medical research. NGS technologies have also made a huge and ongoing impact on transcriptome, gene annotation and RNA splice identification in addition to the traditional applications of DNA sequencing in genome resequencing and SNP discovery, Metagenomic 8 and genome methylation analysis 9 have also benefited from these new technologies. A new applications is also likely to be unveiled in the coming years.…”

Section: Introductionmentioning

confidence: 99%

Evaluation of next-generation sequencing software in mapping and assembly

et al. 2011

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Next-generation high-throughput DNA sequencing technologies have advanced progressively in sequence-based genomic research and novel biological applications with the promise of sequencing DNA at unprecedented speed. These new non-Sanger-based technologies feature several advantages when compared with traditional sequencing methods in terms of higher sequencing speed, lower per run cost and higher accuracy. However, reads from next-generation sequencing (NGS) platforms, such as 454/Roche, ABI/SOLiD and Illumina/Solexa, are usually short, thereby restricting the applications of NGS platforms in genome assembly and annotation. We presented an overview of the challenges that these novel technologies meet and particularly illustrated various bioinformatics attempts on mapping and assembly for problem solving. We then compared the performance of several programs in these two fields, and further provided advices on selecting suitable tools for specific biological applications.

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“…The development of DNA chips for genome-wide expression studies [2] and the next generation sequencing (NGS) technology for much deeper transcriptome analyses [3] are complementary approaches to conduct functional genomics research [4]. DNA chip-based transcriptome analyses are efficient to study host-pathogen interactions using either pathogen transcriptomes [5] or host transcriptomes [6-9] or both pathogen and host modifications of the transcriptome during infection [10].…”

Section: Introductionmentioning

confidence: 99%

Transcriptome analysis of porcine PBMCs after in vitro stimulation by LPS or PMA/ionomycin using an expression array targeting the pig immune response

et al. 2010

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BackgroundDesigning sustainable animal production systems that better balance productivity and resistance to disease is a major concern. In order to address questions related to immunity and resistance to disease in pig, it is necessary to increase knowledge on its immune system and to produce efficient tools dedicated to this species.ResultsA long-oligonucleotide-based chip referred to as SLA-RI/NRSP8-13K was produced by combining a generic set with a newly designed SLA-RI set that targets all annotated loci of the pig major histocompatibility complex (MHC) region (SLA complex) in both orientations as well as immunity genes outside the SLA complex.The chip was used to study the immune response of pigs following stimulation of porcine peripheral blood mononuclear cells (PBMCs) with lipopolysaccharide (LPS) or a mixture of phorbol myristate acetate (PMA) and ionomycin for 24 hours. Transcriptome analysis revealed that ten times more genes were differentially expressed after PMA/ionomycin stimulation than after LPS stimulation. LPS stimulation induced a general inflammation response with over-expression of SAA1, pro-inflammatory chemokines IL8, CCL2, CXCL5, CXCL3, CXCL2 and CCL8 as well as genes related to oxidative processes (SOD2) and calcium pathways (S100A9 and S100A12). PMA/ionomycin stimulation induced a stronger up-regulation of T cell activation than of B cell activation with dominance toward a Th1 response, including IL2, CD69 and TNFRSF9 (tumor necrosis factor receptor superfamily, member 9) genes. In addition, a very intense repression of THBS1 (thrombospondin 1) was observed. Repression of MHC class I genes was observed after PMA/ionomycin stimulation despite an up-regulation of the gene cascade involved in peptide processing. Repression of MHC class II genes was observed after both stimulations. Our results provide preliminary data suggesting that antisense transcripts mapping to the SLA complex may have a role during immune response.ConclusionThe SLA-RI/NRSP8-13K chip was found to accurately decipher two distinct immune response activations of PBMCs indicating that it constitutes a valuable tool to further study immunity and resistance to disease in pig. The transcriptome analysis revealed specific and common features of the immune responses depending on the stimulation agent that increase knowledge on pig immunity.

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Applications of next-generation sequencing technologies in functional genomics

Cited by 1,008 publications

References 110 publications

Genetics and Genetic Testing in Congenital Heart Disease

Genetics and Genetic Testing in Congenital Heart Disease

Evaluation of next-generation sequencing software in mapping and assembly

Transcriptome analysis of porcine PBMCs after in vitro stimulation by LPS or PMA/ionomycin using an expression array targeting the pig immune response

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